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Old 01-02-2012, 02:23 PM   #1
Location: FL

Join Date: Dec 2008
Posts: 26
Default How to do CASAVA alignment by using fastq files

Hi, I am trying to make CASAVA1.8 work.

The company give me the demultiplexing data (in fastq format), Can some one please let me know how to do the alignment with CASAVA1.8?

I am very confused with all different folders created by CASAVA. can I run casava directly by only input the fastq files and the references? If not, may I know what kind of folder structure should I prepare for it able to process?

Thanks a lot and happy new year!!!
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